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- PDB-8y4v: Crystal structure of ferric iron-binding protein (FecB) from Vibr... -

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Basic information

Entry
Database: PDB / ID: 8y4v
TitleCrystal structure of ferric iron-binding protein (FecB) from Vibrio alginolyticus in complex with citrate
ComponentsABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / Vibrio alginolyticus / periplasmic binding protein / ferric citrate
Function / homology: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / outer membrane-bounded periplasmic space / CITRATE ANION / ABC transporter substrate-binding protein
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsJiang, J.Y. / Lu, P. / Nagata, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05771 Japan
Japan Society for the Promotion of Science (JSPS)JP20K22561 Japan
Japan Science and TechnologyJPMJSP2108 Japan
Other privateJapan Science and Technology Agency2023-4016
CitationJournal: To Be Published
Title: Crystal structure of ferric iron-binding protein (FecB) from Vibrio alginolyticus in complex with citrate
Authors: Jiang, J.Y. / Lu, P. / Nagata, K.
History
DepositionJan 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
B: ABC transporter substrate-binding protein
C: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2984
Polymers91,1093
Non-polymers1891
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.889, 132.844, 158.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ABC transporter substrate-binding protein


Mass: 30369.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: HKB16_09180 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: A0A7Y0SGI3
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM NaOAc pH 4.5, 24% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→42.66 Å / Num. obs: 36899 / % possible obs: 98.5 % / Redundancy: 3.47 % / Biso Wilson estimate: 29.74 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.09
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 11088 / CC1/2: 0.703 / Rpim(I) all: 0.277 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5058: ???)refinement
HKL-2000data scaling
REFMACphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→42.66 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 1863 5.05 %
Rwork0.2167 35036 -
obs0.2182 36899 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.13 Å2
Refinement stepCycle: LAST / Resolution: 2.31→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 0 296 6723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.486
X-RAY DIFFRACTIONf_dihedral_angle_d14.2672468
X-RAY DIFFRACTIONf_chiral_restr0.0391020
X-RAY DIFFRACTIONf_plane_restr0.0041155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.34561370.2712588X-RAY DIFFRACTION98
2.37-2.440.31541450.2742695X-RAY DIFFRACTION100
2.44-2.520.26181220.25822651X-RAY DIFFRACTION100
2.52-2.610.32241520.26012684X-RAY DIFFRACTION100
2.61-2.720.3541400.27472566X-RAY DIFFRACTION97
2.72-2.840.26241430.2422694X-RAY DIFFRACTION100
2.84-2.990.27551380.22682706X-RAY DIFFRACTION100
2.99-3.180.23871240.22222691X-RAY DIFFRACTION100
3.18-3.420.25961540.22982680X-RAY DIFFRACTION100
3.42-3.770.23681500.20872677X-RAY DIFFRACTION98
3.77-4.310.22911460.18722724X-RAY DIFFRACTION99
4.31-5.430.19481510.17922751X-RAY DIFFRACTION100
5.43-42.660.19681610.18622929X-RAY DIFFRACTION100

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